Mr. Shawn Doan, science teacher at Sehome High School in Bellingham (Washington), gives answers to a selection of questions asked by his students during a number of video conferences between him on the R/V Thompson and his students on land.

How do bacteria get energy from rusting iron?

You have all seen iron rust. Leave something iron outside in the rain and rust will slowly appear. If left long enough, the rust will totally consume the iron. The fact that metallic iron is converted to rust spontaneously means there is more energy in the metallic iron than in the rust. (If not, we’d find rust spontaneously turning to metallic iron.) The amount of energy is very small and is released very slowly, but if bacteria can control it then they have a chance to capture the energy that is released. This is what the iron oxidizing bacteria are able to do.

The best source of iron for bacteria is a source they can easily absorb - dissolved iron. To dissolve iron in water, the water has to have all the oxygen removed. If any oxygen remained in the water the iron would just combine with it to form rust and all the energy would be lost before bacteria could use it. You may have seen this in the sides of ditches where you can see a rusty stain.

Volcanic hot springs are one source of dissolved iron. A single bacterium living on the edge of the iron-rich water can absorb both iron and oxygen and keep them separate until it can get the energy from their combination. When the bacterium finally allows the iron and oxygen to combine, it does so in a metabolic pathway that captures the energy released during their combination. Humans don’t have this type of metabolism so are unable to use iron for energy. After the combination of iron and oxygen the bacteria must get rid of the iron oxide that results, consequently large volumes of rust build up around the bacterial mats.

Are iron-oxidizing bacteria found only at Loi’hi?

No, it is probable that bacteria like those found at Loi’hi are found throughout the oceans. Historically iron-oxidizing bacteria have been found only where dissolved iron is associated with acidic water. What hadn’t been known until recently is that some iron-oxidizers could survive where the water was not acidic – that they could survive in seawater. Seawater is not acidic, instead it is slightly basic. Loi’hi is an ideal place to look for these bacteria because Loi’hi water contains lots of dissolved iron. The basalt in the ocean crust is also a source of iron, so Loi’hi can serve as a model for iron-oxidizers throughout ocean basins.

Do volcanic eruptions affect the type of bacteria that are found? How?

Yes. Changing water temperature changes the water chemistry, so hot water will have different minerals dissolved in it than cooler water. And different types of chemosynthetic bacteria need different types of chemicals dissolved in the water. (Chemosynthetic means the bacteria can use chemicals dissolved in water for energy to make food in much the same way that photosynthetic means an organism can use light for energy to make food.) Some bacteria can get energy to make food from sulfur compounds, some from iron compounds and some from manganese compounds. The temperature of the water in contact with the rock determines which chemicals will dissolve – hotter water dissolves different chemicals than cooler water. So any volcanic activity that changes the temperature of the water coming out of the vent can affect the type of bacteria that can survive. Eruptions certainly affect water temperatures.

Eruptions can burn or bury any organisms living on the seafloor, including bacteria. Bacteria can also be cut off from their energy source if it is a hot water vent. Iron oxidizing bacteria need dissolved iron as well as some seawater to live and grow. If the eruption cuts off the flow of water, or changes its temperature too much, the bacteria will die. Even if the water chemistry and temperature change only slightly, it is likely that other competing bacteria will replace those that were there before the eruption.

So, how can the chemistry of the water change, if it all starts as seawater and if it’s all going through the same rock? The temperature. A pulse of lava pushed into the volcano can increase the temperature of the water. Hotter water dissolves different minerals than cooler water. You know that some candies dissolve easily in cold water and others don’t. Those that don’t can be made to dissolve faster by heating the water.

How are the bacteria preserved?

Bacterial samples can be frozen at -80° Celsius (using liquid Nitrogen) or preserved with chemicals, such as paraformaldehyde, gluteraldehyde or ethanol. They can also be preserved in a slow growing culture and refrigerated for shipment.

How do you keep the bacteria alive on the way to the surface?

Once the bacteria get away from the hot vent they quickly cool to the temperature of surrounding deep seawater – about 2° Celsius (35 °F). This shuts down the metabolism of bacteria that are used to being warmed by the vent fluids. The samples are put in sample boxes (bioboxes) on Jason or the deep sea elevator that prevent the samples from warming too quickly on the Hawaiian surface.

Have there been any new discoveries this year?

Yes, sonar mapping of the pit crater (Pele’s Pit) revealed an area venting hot water that was previously unknown. If the chemistry of the water coming out of these new vents is different than other vents, it may have a completely different community of microbes growing there. Bacterial traps and samplers have been deployed. A survey at the deep site (FeMO Deep) revealed new areas of bacterial mat. The deep mats have a manganese crust that is being analyzed by Brad Tebo’s lab for the presence of Manganese Oxidizing bacteria. Hypothetically there is more energy available in manganese oxidation than in iron oxidation, but it has not yet been demonstrated conclusively that any bacteria use manganese oxidizing metabolism as their principle energy source. A new technique of growing iron oxidizing bacteria under the microscope is being developed by Clara Chan. Her cultures showed some growth, which is remarkable considering that any presence of oxygen will make the iron unavailable to the bacteria.

What are some recent FeMO discoveries?

The existence of iron oxidizing bacteria in the ocean at near neutral pH is a recent discovery. The FeMO work demonstrates their prevalence in the deep sea. Dave Emerson and Craig Moyer have been able to culture and genetically describe the iron oxidizer Mariprofundus ferrooxydans, an organism new to science. Microbiologists are learning to grow bacteria that grow within the surface of volcanic glass. It appears that (though it is still controversial) that bacteria can colonize cooled-off volcanic glass, and tunnel into it, in search of chemicals they require for their growth. Some of these tunnels are found in ancient basalt rock billions of years old, as recently found by Hubert Staudigel and co-workers. The tunneling of the bacteria contributes to the weathering of the ocean crust, hence the phrase “Rust the Crust”. Work by Mark Kurz demonstrates that a new anaerobic rock sampling technique works to preserve rock samples for analysis of primordial noble gases (gasses such as Helium, Argon and Krypton that have existed since the Earth formed).

What is the purpose of Medea?

Medea hangs on the wire between Jason and the ship. Due to the weight of Medea the winch wire is tight between Medea and the ship. Between Medea and Jason the wire is slack so Jason can move around freely. The slack between Medea and Jason also allows Medea to bob up and down with the surge of the ship so that no ship movement is transferred to Jason when delicate work is being done.

Have we seen an active eruption at Lo’ihi?

No, unless you want to call the hot springs an eruption. But a couple years ago Craig Moyer was using Jason on a seamount in the Marianas volcanic arc during an eruption. He described how lava was flowing in the crater and large chunks of it were being shot into the water column above the crater. The pilot set Jason down near the vent to sample and the crust cracked and Jason started to settle into a pool of molten sulfur. Craig said the hardened sulfur was very difficult to remove from Jason’s skids.

How many people are needed to operated Jason?

Jason is sent out with 10 technicians that work rotating shifts to operate and maintain it.

How deep can Jason go?

Jason is capable of going 6,000 meters deep. This is nearly 20,000 feet deep and corresponds to 600 atmospheres of pressure.

How long can Jason stay under water?

Jason has stayed underwater for days. On dive #365, Jason has been down for over 50 hours and it is still down. The Jason techs and scientists work 4 hour shifts to operate Jason for the duration of the dive.

Have there been any Jason failures?

They are very rare. Jason is scheduled to dive about 150 days per year. There was one failure during the FeMO 2007 dive series that ended a dive early when the fiber-optic cable between Jason and Medea failed. Jason was pulled aboard and the cable replaced. There have been two minor failures during our first dive this year: One arm carrying a sample box (“Biobox”) failed to deploy so the box was unusable. And the sonar failed. Neither failure was severe enough to cause the end of the dive. Jason kept working. Dive #370 was cut short because of a communications failure with Medea. However, the problem was solved quickly and the Jason returned to Loihi's depth within 8 hours.

How much force would it take to lift the deep sea elevator now that its floats have imploded?

Liquids do not compress under pressure so their density does not change with depth. (Unlike the atmosphere which does compress resulting in greater density at lower elevations.)  Consequently in the ocean the lifting force does not depend on depth, only the density of seawater. (If seawater did compress things might sink half way to the bottom and drift around on a layer of ocean equal to their density.) The buoyancy of each of the glass floats on the elevator is about 25 kg (55 pounds) and there are 8 floats, so the elevator weighs about 200 kg (440 lbs) extra now that the floats have collapsed. The elevator was put down with extra weight so it would sink. Jason could remove this weight and the elevator would require less than 200 kg to lift it until it reached the air. In the air the elevator would weigh much more.

One reason to leave the elevator on the bottom is that the glass in the floats has been pulverized into fine shards that are dangerous and difficult to clean up. Clumps of these shards can be seen in the photographs as white specks scattered around the sunken elevator.

How does the R/V Thompson make power?

The Thompson has 3 large 16 cylinder diesel engines powering three 1,500 kilowatt generators. These 3 diesel-generator sets are the main power for the two 3,000 horsepower electric motors that turn the propellers. While holding station with dynamic positioning only one of the diesel-generator sets is required. At cruising speed 2 diesel generator sets will be used. The Thompson also has 3 smaller 750 kW diesel-generator sets that make electricity for the navigational equipment, water maker, sewage pumps, computers, scientific instruments and Jason and Medea. Light loads such as holding station require only 1 large diesel-generator set and one small diesel-generator set.

How much fuel does the R/V Thompson burn each day?

This trip the Thompson has been using about 1,600 gallons of diesel fuel per day while on station. This energy keeps the ship on station (dynamic positioning) and provides all the power for navigation, radar, sonar, lights, water maker, sewage treatment, scientific instruments, computers, as well as Jason and Medea. At a cruising speed of 11 knots the R/V Thompson uses about 3,000 gallons per day. The fuel capacity of the Thompson is 275,000 gallons.

How many people are aboard the R/V Thompson?

There are 57 people aboard including 25 in the science party, 10 Jason technicians and 22 ship’s crew.

What is done with the sewage?

Sewage is stored in a tank then run through a sewage treatment plant similar to sewage treatment plants ashore.

What is Mr. Doan’s Job while at sea?

Mr. Doan’s primary job is to connect students to scientists by organizing communication between the ship and his biology classes at Sehome High School. This has been done in live conversations via the internet, via short videos made during the cruise and via illustrated text based communication.

The text based communication takes several forms. Mr. Doan has recorded student questions and composed answers (like this one) for posting on the FeMO website. He has encouraged scientists to write explanations of their work for student readers with the result that several of these reports are now on the FeMO website. He writes daily reports describing the day to day science and activities aboard the R/V Thompson. Mr. Doan also takes photos of activities and personnel aboard the R/V Thompson to illustrate these activities. All of these photos must be organized into photo libraries and a detailed description written for each.

Mr. Doan’s responsibilities toward the science include working as a data logger for the Jason (he has the 8pm to midnight shift in the control van), converting the Dive Notebooks and Sample Logs to digital PDF files for use by researchers, and organizing dive photos and recording the Jason event numbers that correspond to those photos.

Shawn Doan onboard the R/V Thomas G. Thompson
8 October, 2008

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